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Factors affecting the relative abundance of nuclear copies of mitochondrial DNA (numts) in hominoids.

ABSTRACT: Although nuclear copies of mitochondrial DNA (numts) can originate from any portion of the mitochondrial genome, evidence from humans suggests that more variable parts of the mitochondrial genome, such as the mitochondrial control region (MCR), are under-represented in the nucleus. This apparent deficit might arise from the erosion of sequence identity in numts originating from rapidly evolving mitochondrial sequences. However, the extent to which mitochondrial sequence properties impacts the number of numts detected in genomic surveys has not been evaluated. In order to address this question, we: (1) conducted exhaustive BLAST searches of MCR numts in three hominoid genomes; (2) assessed numt prevalence across the four MCR sub-domains (HV1, CCD, HV2, and MCR(F)); (3) estimated their insertion rates in great apes (Hominoidea); and (4) examined the relationship between mitochondrial DNA variability and numt prevalence in sequences originating from MCR and coding regions of the mitochondrial genome. Results indicate a marked deficit of numts from HV2 and MCR(F) MCR sub-domains in all three species. These MCR sub-domains exhibited the highest proportion of variable sites and the lowest number of detected numts per mitochondrial site. Variation in MCR insertion rate between lineages was also observed with a pronounced burst in recent integrations within chimpanzees and orangutans. A deficit of numts from HV2/MCR(F) was observed regardless of age, whereas HV1 is under-represented only in older numts (>25 million years). Finally, more variable mitochondrial genes also exhibit a lower identity with nuclear copies and because of this, appear to be under-represented in human numt databases.

SUBMITTER: Soto-Calderon ID

PROVIDER: S-EPMC3508264 | biostudies-literature | 2012 Oct

REPOSITORIES: biostudies-literature

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Factors affecting the relative abundance of nuclear copies of mitochondrial DNA (numts) in hominoids.

Soto-Calderón I D ID Lee E J EJ Jensen-Seaman M I MI Anthony N M NM

Journal of molecular evolution 20121010 3-4

Although nuclear copies of mitochondrial DNA (numts) can originate from any portion of the mitochondrial genome, evidence from humans suggests that more variable parts of the mitochondrial genome, such as the mitochondrial control region (MCR), are under-represented in the nucleus. This apparent deficit might arise from the erosion of sequence identity in numts originating from rapidly evolving mitochondrial sequences. However, the extent to which mitochondrial sequence properties impacts the nu ...[more]

PMID: 23053193

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Project description:The first hyper-variable region (HV1) of the mitochondrial control region (MCR) has been widely used as a molecular tool in population genetics, but inadvertent amplification of nuclear translocated copies of mitochondrial DNA (numts) in gorillas has compromised the use of mitochondrial DNA in population genetic studies. At least three putative classes (I, II, III) of gorilla-specific HV1 MCR numts have been uncovered over the past decade. However, the number, size and location of numt loci in gorillas and other apes are completely unknown. Furthermore, little work to date has assessed the utility of numts as candidate population genetic markers. In the present study, we screened Bacterial Artificial Chromosome (BAC) genomic libraries in the chimpanzee and gorilla to compare patterns of mitochondrial-wide insertion in both taxa. We conducted an intensive BLAST search for numts in the gorilla genome and compared the prevalence of numt loci originating from the MCR with other great ape taxa. Additional gorilla-specific MCR numts were retrieved either through BAC library screens or using an anchored-PCR (A-PCR) amplification using genomic DNA from five unrelated gorillas. Locus-specific primers were designed to identify numt insertional polymorphisms and evaluate their potential as population genetic markers. Mitochondrial-wide surveys of chimpanzee and gorilla BACs showed that the number of numts does not differ between these two taxa. However, MCR numts are more abundant in chimpanzees than in other great apes. We identified and mapped 67 putative gorilla-specific numts, including two that contain the entire HV1 domain, cluster with sequences from two numt classes (I, IIb) and will likely co-amplify with mitochondrial sequences using most published HV1 primers. However, phylogenetic analysis coupled with post-hoc analysis of mitochondrial variation can successfully differentiate nuclear sequences. Insertional polymorphisms were evident in three out of five numts examined, indicating their potential utility as molecular markers. Taken together, these findings demonstrate the potentially powerful insight that numts could make in uncovering population history in gorillas and other mammals.

Dataset Information

Factors affecting the relative abundance of nuclear copies of mitochondrial DNA (numts) in hominoids.

Publications

Factors affecting the relative abundance of nuclear copies of mitochondrial DNA (numts) in hominoids.

Similar Datasets

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